Implement Binary Upload (Fixes #2126) - WIP

modules/rest-api/src/blaze/rest_api/routes.clj

@@ -35,6 +35,10 @@
   {:name :auth-guard
    :wrap auth-guard/wrap-auth-guard})
 
+(def ^:private wrap-binary-resource
+  {:name :resource
+   :wrap resource/wrap-binary-resource})
+
 (def ^:private wrap-resource
   {:name :resource
    :wrap resource/wrap-resource})
@@ -103,6 +107,8 @@
       {:fhir.resource/type name}
       [""
        (cond-> {:name (keyword name "type")}
+         (= name "Binary")
+         (assoc :response-type :binary)
          (contains? interactions :search-type)
          (assoc :get {:interaction "search-type"
                       :middleware [[wrap-db node db-sync-timeout]
@@ -111,7 +117,9 @@
                                    :blaze.rest-api.interaction/handler)})
          (contains? interactions :create)
          (assoc :post {:interaction "create"
-                       :middleware [wrap-resource]
+                       :middleware (if (:response-type :binary)
+                                     [wrap-binary-resource]
+                                     [wrap-resource])
                        :handler (-> interactions :create
                                     :blaze.rest-api.interaction/handler)})
          (contains? interactions :conditional-delete-type)
@@ -179,7 +187,9 @@
                                       :blaze.rest-api.interaction/handler)})
             (contains? interactions :update)
             (assoc :put {:interaction "update"
-                         :middleware [wrap-resource]
+                         :middleware (if (:response-type :binary)
+                                       [wrap-binary-resource]
+                                       [wrap-resource])
                          :handler (-> interactions :update
                                       :blaze.rest-api.interaction/handler)})
             (contains? interactions :delete)

modules/rest-util/src/blaze/middleware/fhir/resource.clj

@@ -7,6 +7,7 @@
    [blaze.anomaly :as ba :refer [if-ok when-ok]]
    [blaze.async.comp :as ac]
    [blaze.fhir.spec :as fhir-spec]
+   [blaze.fhir.spec.type :as type]
    [clojure.data.xml.jvm.parse :as xml-jvm]
    [clojure.data.xml.tree :as xml-tree]
    [clojure.java.io :as io]
@@ -17,6 +18,7 @@
   (:import
    [com.ctc.wstx.api WstxInputProperties]
    [java.io Reader]
+   [java.util Base64 Base64$Encoder]
    [javax.xml.stream XMLInputFactory]))
 
 (set! *warn-on-reflection* true)
@@ -95,6 +97,29 @@
       (assoc request :body resource))
     (ba/incorrect "Missing HTTP body.")))
 
+(def ^:private ^Base64$Encoder b64-encoder
+  (.withoutPadding (Base64/getUrlEncoder)))
+
+(defn- resource-request-binary** [data]
+  (with-open [_ (prom/timer parse-duration-seconds "binary")]
+    (.encodeToString b64-encoder data)))
+
+(defn- binary-content-type [body]
+  (or (-> body :contentType type/value)
+      "application/octet-stream"))
+
+(defn- resource-request-binary* [{:keys [data contentType] :as body}]
+  (when data
+    (assoc body
+           :data (resource-request-binary** data)
+           :contentType (binary-content-type contentType))))
+
+(defn- resource-request-binary [{:keys [body] :as request}]
+  (if body
+    (when-ok [resource (resource-request-binary* body)]
+      (assoc request :body resource))
+    (ba/incorrect "Missing HTTP body.")))
+
 (defn- unsupported-media-type-msg [media-type]
   (format "Unsupported media type `%s` expect one of `application/fhir+json` or `application/fhir+xml`."
           media-type))
@@ -125,3 +150,29 @@
     (if-ok [request (resource-request request)]
       (handler request)
       ac/completed-future)))
+
+(defn- binary-resource-request [request]
+  (if-let [content-type (request/content-type request)]
+    (cond
+      (json-request? content-type) (resource-request-json request)
+      (xml-request? content-type) (resource-request-xml request)
+      :else
+      (resource-request-binary request))
+    (if (str/blank? (slurp (:body request)))
+      (assoc request :body nil)
+      (ba/incorrect "Content-Type header expected, but is missing."))))
+
+(defn wrap-binary-resource
+  "Middleware to parse a binary resource from the body according the content-type
+  header.
+
+  Updates the :body key in the request map on successful parsing and conforming
+  the resource to the internal format.
+
+  Returns an OperationOutcome in the internal format, skipping the handler, with
+  an appropriate error on parsing and conforming errors."
+  [handler]
+  (fn [request]
+    (if-ok [request (binary-resource-request request)]
+      (handler request)
+      ac/completed-future)))

modules/rest-util/test/blaze/middleware/fhir/resource_test.clj

@@ -2,10 +2,13 @@
   (:require
    [blaze.async.comp :as ac]
    [blaze.fhir.spec :as fhir-spec]
+   [blaze.fhir.spec.type :as type]
    [blaze.fhir.test-util]
    [blaze.handler.util :as handler-util]
-   [blaze.middleware.fhir.resource :refer [wrap-resource]]
+   [blaze.middleware.fhir.resource :refer [wrap-binary-resource wrap-resource]]
    [blaze.test-util :as tu :refer [satisfies-prop]]
+   [clojure.data.xml :as xml]
+   [clojure.java.io :as io]
    [clojure.spec.test.alpha :as st]
    [clojure.string :as str]
    [clojure.test :as test :refer [deftest is testing]]
@@ -23,18 +26,31 @@
 
 (test/use-fixtures :each tu/fixture)
 
-(defn wrap-error [handler]
+(defn- wrap-error [handler]
   (fn [request]
     (-> (handler request)
         (ac/exceptionally handler-util/error-response))))
 
-(def resource-handler
-  "A handler which just returns the :body from the request."
+(defn- parse-json [body]
+  (fhir-spec/conform-json (fhir-spec/parse-json body)))
+
+(defn- parse-xml [body]
+  (with-open [reader (io/reader body)]
+    (fhir-spec/conform-xml (xml/parse reader))))
+
+(def ^:private resource-handler
+  "A handler which just returns the `:body` from a non-binary resource request."
   (-> (comp ac/completed-future :body)
       wrap-resource
       wrap-error))
 
-(defn input-stream
+(def ^:private binary-resource-handler
+  "A handler which just returns the `:body` from a binary resource request."
+  (-> (comp ac/completed-future :body)
+      wrap-binary-resource
+      wrap-error))
+
+(defn- input-stream
   ([^String s]
    (ByteArrayInputStream. (.getBytes s StandardCharsets/UTF_8)))
   ([^String s closed?]
@@ -193,6 +209,33 @@
               :body (input-stream (str "<Binary xmlns=\"http://hl7.org/fhir\"><data value=\"" (apply str (repeat (* 8 1024 1024) \a)) "\"/></Binary>"))})
       fhir-spec/fhir-type := :fhir/Binary)))
 
+(deftest binary-test
+  (testing "returning the FHIR resource (both as JSON and as XML)"
+    (let [binary-data "MTA1NjE0Cg=="]
+      (doseq [[content-type body-parser resource-string-representation]
+              [["application/fhir+json;charset=utf-8" parse-json (str "{\"data\" : \"" binary-data "\", \"resourceType\" : \"Binary\"}")]
+               ["application/fhir+xml;charset=utf-8" parse-xml (str "<Binary xmlns=\"http://hl7.org/fhir\"><data value=\"" binary-data "\"/></Binary>")]]]
+        (let [closed? (atom false)]
+          (given @(binary-resource-handler
+                   {:headers {"content-type" content-type}
+                    :body (input-stream resource-string-representation closed?)})
+            :status := 200
+            identity := "this is what I get"
+            fhir-spec/fhir-type := :fhir/Binary
+            [:headers "Content-Type"] := content-type
+            [:body body-parser] := {:fhir/type :fhir/Binary
+                                    :contentType (type/code content-type)
+                                    :data #fhir/base64Binary"MTA1NjE0Cg=="}))))))
+
+(comment
+  (str "{\"data\" : \"" "MTA1NjE0Cg==" "\", \"resourceType\" : \"Binary\"}")
+  ;; => "{\"data\" : \"MTA1NjE0Cg==\", \"resourceType\" : \"Binary\"}"
+
+  (str "<Binary xmlns=\"http://hl7.org/fhir\"><data value=\"" "MTA1NjE0Cg==" "\"/></Binary>")
+  ;; => "<Binary xmlns=\"http://hl7.org/fhir\"><data value=\"MTA1NjE0Cg==\"/></Binary>"
+
+  :end)
+
 (def ^:private whitespace
   (gen/fmap str/join (gen/vector (gen/elements [" " "\n" "\r" "\t"]))))